5-1878451-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016358.3(IRX4):c.1078G>A(p.Ala360Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,459,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016358.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRX4 | NM_016358.3 | c.1078G>A | p.Ala360Thr | missense_variant | 5/5 | ENST00000231357.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRX4 | ENST00000231357.7 | c.1078G>A | p.Ala360Thr | missense_variant | 5/5 | 1 | NM_016358.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000503 AC: 3AN: 59586Hom.: 0 AF XY: 0.0000954 AC XY: 3AN XY: 31450
GnomAD4 exome AF: 0.0000734 AC: 96AN: 1307078Hom.: 0 Cov.: 33 AF XY: 0.0000737 AC XY: 47AN XY: 637560
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | The c.1078G>A (p.A360T) alteration is located in exon 5 (coding exon 5) of the IRX4 gene. This alteration results from a G to A substitution at nucleotide position 1078, causing the alanine (A) at amino acid position 360 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at